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JAL-2473 removed unused fields in JalviewDialog
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
GeneDbSource.java
diff --git
a/src/jalview/ws/dbsources/GeneDbSource.java
b/src/jalview/ws/dbsources/GeneDbSource.java
index
2a3d7bb
..
ce21ad0
100644
(file)
--- a/
src/jalview/ws/dbsources/GeneDbSource.java
+++ b/
src/jalview/ws/dbsources/GeneDbSource.java
@@
-1,37
+1,29
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
*/
package jalview.ws.dbsources;
-import java.io.File;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.StringTokenizer;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.xdb.embl.EmblEntry;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
+
+import com.stevesoft.pat.Regex;
/**
* Test class for accessing GeneDB - not yet finished.
/**
* Test class for accessing GeneDB - not yet finished.
@@
-39,13
+31,12
@@
import jalview.ws.seqfetcher.DbSourceProxyImpl;
* @author JimP
*
*/
* @author JimP
*
*/
-public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
+public class GeneDbSource extends EmblXmlSource
{
public GeneDbSource()
{
{
public GeneDbSource()
{
- addDbSourceProperty(DBRefSource.DNASEQDB);
- addDbSourceProperty(DBRefSource.CODINGSEQDB);
+ super();
}
/*
}
/*
@@
-53,6
+44,7
@@
public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
+ @Override
public String getAccessionSeparator()
{
// TODO Auto-generated method stub
public String getAccessionSeparator()
{
// TODO Auto-generated method stub
@@
-64,6
+56,7
@@
public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
+ @Override
public Regex getAccessionValidator()
{
// TODO Auto-generated method stub
public Regex getAccessionValidator()
{
// TODO Auto-generated method stub
@@
-75,6
+68,7
@@
public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
+ @Override
public String getDbSource()
{
return DBRefSource.GENEDB;
public String getDbSource()
{
return DBRefSource.GENEDB;
@@
-85,6
+79,7
@@
public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
*
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
+ @Override
public String getDbVersion()
{
// TODO Auto-generated method stub
public String getDbVersion()
{
// TODO Auto-generated method stub
@@
-96,6
+91,7
@@
public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
*
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
+ @Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
// query of form
public AlignmentI getSequenceRecords(String queries) throws Exception
{
// query of form
@@
-109,6
+105,7
@@
public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
+ @Override
public boolean isValidReference(String accession)
{
// TODO Auto-generated method stub
public boolean isValidReference(String accession)
{
// TODO Auto-generated method stub
@@
-118,13
+115,21
@@
public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
/**
* return T.Brucei Mannosyl-Transferase TbPIG-M
*/
/**
* return T.Brucei Mannosyl-Transferase TbPIG-M
*/
+ @Override
public String getTestQuery()
{
return "Tb927.6.3300";
}
public String getTestQuery()
{
return "Tb927.6.3300";
}
+ @Override
public String getDbName()
{
return "GeneDB"; // getDbSource();
}
public String getDbName()
{
return "GeneDB"; // getDbSource();
}
+
+ @Override
+ public int getTier()
+ {
+ return 0;
+ }
}
}